# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dan Blankenberg dan@bx.psu.edu # Date 1275939260 14400 # Node ID 37f4420ba3fcf9eb0fd097cf812ad91cc2824f99 # Parent 7de1adaf5628e04e2da0d948f03d08cb5ce5d7f3 Bug fix for handling 'spaces to tab' for non-binary composite datatype files. Add upload tests for testing 'space to tab' when uploading composite and non-composite datatypes.
--- a/test/functional/test_get_data.py +++ b/test/functional/test_get_data.py @@ -4,14 +4,16 @@ from galaxy.model.mapping import context from base.twilltestcase import TwillTestCase
class UploadData( TwillTestCase ): - def test_0005_upload_file( self ): - """Test uploading 1.bed, NOT setting the file format""" + def test_0000_setup_upload_tests( self ): + """Configuring upload tests, setting admin_user""" self.logout() self.login( email='test@bx.psu.edu' ) global admin_user admin_user = sa_session.query( galaxy.model.User ) \ .filter( galaxy.model.User.table.c.email=='test@bx.psu.edu' ) \ .one() + def test_0005_upload_file( self ): + """Test uploading 1.bed, NOT setting the file format""" history = sa_session.query( galaxy.model.History ) \ .filter( and_( galaxy.model.History.table.c.deleted==False, galaxy.model.History.table.c.user_id==admin_user.id ) ) \ @@ -25,6 +27,21 @@ class UploadData( TwillTestCase ): self.verify_dataset_correctness( '1.bed', hid=str( hda.hid ) ) self.check_history_for_string( "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>" ) self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0006_upload_file( self ): + """Test uploading 1.bed.spaces, with space to tab selected, NOT setting the file format""" + history = sa_session.query( galaxy.model.History ) \ + .filter( and_( galaxy.model.History.table.c.deleted==False, + galaxy.model.History.table.c.user_id==admin_user.id ) ) \ + .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ + .first() + self.upload_file( '1.bed.spaces', space_to_tab = True ) + hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \ + .first() + assert hda is not None, "Problem retrieving hda from database" + self.verify_dataset_correctness( '1.bed', hid=str( hda.hid ) ) + self.check_history_for_string( "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>" ) + self.delete_history( id=self.security.encode_id( history.id ) ) def test_0010_upload_file( self ): """Test uploading 4.bed.gz, manually setting the file format""" self.check_history_for_string( 'Your history is empty' ) @@ -174,15 +191,36 @@ class UploadData( TwillTestCase ): .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ .first() # lped data types include a ped_file and a map_file ( which is binary ) - self.upload_composite_datatype_file( 'lped', ped_file='tinywga.ped', map_file='tinywga.map', base_name='rgenetics' ) + self.upload_file( None, ftype='lped', metadata = [ { 'name':'base_name', 'value':'rgenetics' } ], composite_data = [ { 'name':'ped_file', 'value':'tinywga.ped' }, { 'name':'map_file', 'value':'tinywga.map'} ] ) # Get the latest hid for testing hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \ .first() assert hda is not None, "Problem retrieving hda from database" # We'll test against the resulting ped file and map file for correctness - self.verify_composite_datatype_file_content( 'rgenetics.ped', str( hda.id ) ) - self.verify_composite_datatype_file_content( 'rgenetics.map', str( hda.id ) ) + self.verify_composite_datatype_file_content( 'tinywga.ped', str( hda.id ), base_name = 'rgenetics.ped' ) + self.verify_composite_datatype_file_content( 'tinywga.map', str( hda.id ), base_name = 'rgenetics.map' ) + self.check_history_for_string( "rgenetics" ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0056_upload_file( self ): + """Test uploading lped composite datatype file, manually setting the file format, and using space to tab on one file (tinywga.ped)""" + # Logged in as admin_user + self.check_history_for_string( 'Your history is empty' ) + history = sa_session.query( galaxy.model.History ) \ + .filter( and_( galaxy.model.History.table.c.deleted==False, + galaxy.model.History.table.c.user_id==admin_user.id ) ) \ + .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ + .first() + # lped data types include a ped_file and a map_file ( which is binary ) + self.upload_file( None, ftype='lped', metadata = [ { 'name':'base_name', 'value':'rgenetics' } ], composite_data = [ { 'name':'ped_file', 'value':'tinywga.ped', 'space_to_tab':True }, { 'name':'map_file', 'value':'tinywga.map'} ] ) + # Get the latest hid for testing + hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \ + .first() + assert hda is not None, "Problem retrieving hda from database" + # We'll test against the resulting ped file and map file for correctness + self.verify_composite_datatype_file_content( 'tinywga.ped.space_to_tab', str( hda.id ), base_name = 'rgenetics.ped' ) + self.verify_composite_datatype_file_content( 'tinywga.map', str( hda.id ), base_name = 'rgenetics.map' ) self.check_history_for_string( "rgenetics" ) self.delete_history( id=self.security.encode_id( history.id ) ) def test_0060_upload_file( self ): @@ -195,16 +233,16 @@ class UploadData( TwillTestCase ): .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ .first() # pbed data types include a bim_file, a bed_file and a fam_file - self.upload_composite_datatype_file( 'pbed', bim_file='tinywga.bim', bed_file='tinywga.bed', fam_file='tinywga.fam', base_name='rgenetics' ) + self.upload_file( None, ftype='pbed', metadata = [ { 'name':'base_name', 'value':'rgenetics' } ], composite_data = [ { 'name':'bim_file', 'value':'tinywga.bim' }, { 'name':'bed_file', 'value':'tinywga.bed'}, { 'name':'fam_file', 'value':'tinywga.fam' } ] ) # Get the latest hid for testing hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \ .first() assert hda is not None, "Problem retrieving hda from database" # We'll test against the resulting ped file and map file for correctness - self.verify_composite_datatype_file_content( 'rgenetics.bim', str( hda.id ) ) - self.verify_composite_datatype_file_content( 'rgenetics.bed', str( hda.id ) ) - self.verify_composite_datatype_file_content( 'rgenetics.fam', str( hda.id ) ) + self.verify_composite_datatype_file_content( 'tinywga.bim', str( hda.id ), base_name = 'rgenetics.bim' ) + self.verify_composite_datatype_file_content( 'tinywga.bed', str( hda.id ), base_name = 'rgenetics.bed' ) + self.verify_composite_datatype_file_content( 'tinywga.fam', str( hda.id ), base_name = 'rgenetics.fam' ) self.check_history_for_string( "rgenetics" ) self.delete_history( id=self.security.encode_id( history.id ) ) def test_0065_upload_file( self ):
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--- /dev/null +++ b/test-data/1.bed.spaces @@ -0,0 +1,65 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - +chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + +chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - +chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + +chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + +chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - +chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + +chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - +chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + +chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + +chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - +chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + +chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + +chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - +chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + +chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 -
--- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -295,7 +295,7 @@ class Data( object ): def after_setting_metadata( self, dataset ): """This function is called on the dataset after metadata is set.""" dataset.clear_associated_files( metadata_safe = True ) - def __new_composite_file( self, name, optional = False, mimetype = None, description = None, substitute_name_with_metadata = None, is_binary = False, space_to_tab = True, **kwds ): + def __new_composite_file( self, name, optional = False, mimetype = None, description = None, substitute_name_with_metadata = None, is_binary = False, space_to_tab = False, **kwds ): kwds[ 'name' ] = name kwds[ 'optional' ] = optional kwds[ 'mimetype' ] = mimetype
--- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -143,7 +143,7 @@ class TwillTestCase( unittest.TestCase ) filename = os.path.join( *path ) file(filename, 'wt').write(buffer.getvalue())
- def upload_file( self, filename, ftype='auto', dbkey='unspecified (?)', metadata = None, composite_data = None ): + def upload_file( self, filename, ftype='auto', dbkey='unspecified (?)', space_to_tab = False, metadata = None, composite_data = None ): """Uploads a file""" self.visit_url( "%s/tool_runner?tool_id=upload1" % self.url ) try: @@ -156,9 +156,11 @@ class TwillTestCase( unittest.TestCase ) for i, composite_file in enumerate( composite_data ): filename = self.get_filename( composite_file.get( 'value' ) ) tc.formfile( "1", "files_%i|file_data" % i, filename ) + tc.fv( "1", "files_%i|space_to_tab" % i, composite_file.get( 'space_to_tab', False ) ) else: filename = self.get_filename( filename ) tc.formfile( "1", "file_data", filename ) + tc.fv( "1", "space_to_tab", space_to_tab ) tc.submit("runtool_btn") self.home() except AssertionError, err: @@ -196,60 +198,6 @@ class TwillTestCase( unittest.TestCase ) # Wait for upload processing to finish (TODO: this should be done in each test case instead) self.wait()
- def upload_composite_datatype_file( self, ftype, ped_file='', map_file='', bim_file='', bed_file='', - fped_file='',fphe_file='',pphe_file='',fam_file='',pheno_file='',eset_file='',malist_file='', - affybatch_file='', dbkey='unspecified (?)', base_name='rgenetics' ): - """Tests uploading either of 2 different composite data types ( lped and pbed )""" - self.visit_url( "%s/tool_runner/index?tool_id=upload1" % self.url ) - # Handle refresh_on_change - self.refresh_form( "file_type", ftype ) - tc.fv( "1", "dbkey", dbkey ) - tc.fv( "1", "files_metadata|base_name", base_name ) - if ftype == 'lped': - # lped data types include a ped_file and a map_file - ped_file = self.get_filename( ped_file ) - tc.formfile( "1", "files_0|file_data", ped_file ) - map_file = self.get_filename( map_file ) - tc.formfile( "1", "files_1|file_data", map_file ) - elif ftype == 'pbed': - # pbed data types include a bim_file, a bed_file and a fam_file - bim_file = self.get_filename( bim_file ) - tc.formfile( "1", "files_0|file_data", bim_file ) - bed_file = self.get_filename( bed_file ) - tc.formfile( "1", "files_1|file_data", bed_file ) - fam_file = self.get_filename( fam_file ) - tc.formfile( "1", "files_2|file_data", fam_file ) - elif ftype == 'pphe': - # pphe data types include a phe_file - pphe_file = self.get_filename( pphe_file ) - tc.formfile( "1", "files_0|file_data", pphe_file ) - elif ftype == 'fped': - # fped data types include an fped_file only - fped_file = self.get_filename( fped_file ) - tc.formfile( "1", "files_0|file_data", fped_file ) - elif ftype == 'eset': - # eset data types include a eset_file, a pheno_file - eset_file = self.get_filename( eset_file ) - tc.formfile( "1", "files_0|file_data", eset_file ) - pheno_file = self.get_filename( pheno_file ) - tc.formfile( "1", "files_1|file_data", pheno_file ) - elif ftype == 'affybatch': - # affybatch data types include an affybatch_file, and a pheno_file - affybatch_file = self.get_filename( affybatch_file ) - tc.formfile( "1", "files_0|file_data", affybatch_file ) - pheno_file = self.get_filename( pheno_file ) - tc.formfile( "1", "files_1|file_data", pheno_file ) - else: - raise AssertionError, "Unsupported composite data type (%s) received, currently only %s data types are supported."\ - % (ftype,','.join(self.composite_extensions)) - tc.submit( "runtool_btn" ) - self.check_page_for_string( 'The following job has been succesfully added to the queue:' ) - check_str = base_name #'Uploaded Composite Dataset (%s)' % ftype - self.check_page_for_string( check_str ) - # Wait for upload processing to finish (TODO: this should be done in each test case instead) - self.wait() - self.check_history_for_string( check_str ) - # Functions associated with histories def check_history_for_errors( self ): """Raises an exception if there are errors in a history"""
--- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -241,8 +241,8 @@ class UploadDataset( Group ): name = context.get( 'NAME', None ) info = context.get( 'INFO', None ) warnings = [] - space_to_tab = False - if context.get( 'space_to_tab', None ) not in ["None", None]: + space_to_tab = False + if context.get( 'space_to_tab', None ) not in [ "None", None, False ]: space_to_tab = True file_bunch = get_data_file_filename( data_file, override_name = name, override_info = info ) if file_bunch.path and url_paste: @@ -261,7 +261,7 @@ class UploadDataset( Group ): name = context.get( 'NAME', None ) info = context.get( 'INFO', None ) space_to_tab = False - if context.get( 'space_to_tab', None ) not in ["None", None]: + if context.get( 'space_to_tab', None ) not in [ "None", None, False ]: space_to_tab = True warnings = [] file_bunch = get_data_file_filename( data_file, override_name = name, override_info = info )
--- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -299,7 +299,7 @@ def add_composite_file( dataset, json_fi break elif dataset.composite_file_paths[value.name] is not None: if not value.is_binary: - if value.space_to_tab: + if dataset.composite_file_paths[ value.name ].get( 'space_to_tab', value.space_to_tab ): sniff.convert_newlines_sep2tabs( dataset.composite_file_paths[ value.name ][ 'path' ] ) else: sniff.convert_newlines( dataset.composite_file_paths[ value.name ][ 'path' ] )